CODEWITHSUNDEEP
arraysbashfastq
user2435464
user2435464

Reputation: 3

bash array not working

I am rather new to bioinformatic but trying my best to learn. I am running into an issue and I was hoping someone would know what to do, and explain me how bash tool for multiple file is actually working.

I have a folder with 160 RNAseq libraries unzip just look like name.fastq. I want to run cutadapt (a software which will remove all the adapters sequence from my libraries) on all of them at the same time; so, for one library, the command looks just like this:

python2.6 /imports/home/w/workshop/oibc2013/oibc1/Apps/cutadapt-1.2.1/bin/cutadapt -a name_adapter input_file.fastq > out

So I tried to make a bash array loop to be able to do it on all 160 files I have, but it still does not work.

!/bin/bash

. $HOME/.bashrc
my_array=(*.fastq)
echo ${myarray["SGE_TASK_ID"-1]}
python2.6 \
  /imports/home/w/workshop/oibc2013/oibc1/Apps/cutadapt-1.2.1/bin/cutadapt \
  -a CTGTCTCTTATACACATCT \
  -b AATTGCAGTGGTATCAACGCAGAGCGGCCGC \
  -b GCGGCCGCTCTGCGTTGATACCACTGCAATT \
  -b AAGCAGTGGTATCAACGCAGAGTACATGGG \
  -b CCCATGTACTCTGCGTTGATACCACTGCTT \
  inputs.$SGE_TASK_ID \
  results.$SGE_TASK_ID]}

Upvotes: 0

Views: 437

Answers (1)

IMSoP
IMSoP

Reputation: 97938

Rather than an array, you just want a loop. In this case, since you're matching a glob pattern (*.fastq), a for ... in loop would make sense.

The general syntax is for variable_name in list_of_words; do something_with $variable_name; done;. In your case:

#!/bin/bash
. $HOME/.bashrc

path=/imports/home/w/workshop/oibc2013/oibc1/Apps/cutadapt-1.2.1/bin
for file in *.fastq
do
     python2.6 "$path"/cutadapt -a name_adapter "$file" > "$file.out"
done

Upvotes: 2

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